Genomic-Enhanced EPDs 101
by Joe Epperly
Assistant Executive Director
North American Limousin Foundation
New technology in the beef industry, as always, yields advantages to those who understand and adapt to them. In the past, technologies like EPDs and genetic tests have been at the forefront of beef technologies, but we have now entered the genomic age with an increasing number of tests available to producers and more ways to utilize the resulting information. With these tests come decisions on how to effectively use the technology both in an informational and cost benefit sense.
In order to understand the benefits and limitations of genomic testing, let me give a 30,000-foot overview of how genomic testing and genomic-enhanced EPDs work. A sample is run on a panel that ranges anywhere from 9,000, 50,000, or 80,000 (GGP, HD50K, GGP-HD, respectively) single nucleotide polymorphisms (SNPs) that are evenly spaced across the genome. This panel yields the exact nucleotides at those locations on the genome.
Using known gene affects and the performance information from proven animals run on the HD50K, a profiler was developed through cooperation of NALF, Igenity® (GeneSeek) and Iowa State University. A large majority of these discovery population samples came from the protoporphyria testing done at the University of Missouri in the 1990s through today. This profiler gives a value to each polymorphism at each SNP that relates to a particular trait based on the performance value of animals in the discovery population. These values are an integer that is either positive or negative. We then take these values for each trait, known as molecular breeding values (MBVs), and blend it with the animal’s current EPDs based on the accuracy of both the MBV and EPD.
Now that the background information has been explained, here are the answers to some frequently asked questions on genomic-enhanced EPDs:
What are Genomic Enhanced EPDs (GeEPDs) and what do they do for me?
GeEPDs are when we are comparing the genome of your animal to the genome of the most proven animals in the Limousin population and giving them a relative EPD value based off of the comparison. GeEPDs improve the accuracy of selection. Selection off contemporary group performance data and EPDs has shown itself to be one of the most accurate tools for selection available to breeders, but in the average Limousin herd there just aren’t numbers to form adequate size groups for major EPD shifts. The profiler enhances EPD accuracy and makes it a more reliable tool for selection.
Will this improve my EPDs?
It depends on what you mean by improve. On every animal, the accuracy for every trait will improve and their numbers will change within a standard of possible change for the trait and accuracy of that animal. For example, an animal with a birth weight (BW) EPD of 1.0 with P accuracy has a possible BW EPD range from -2.0 to 4.0. On average, half the animals will go up and half the animals will go down for any particular trait, though most will not move in as extreme a pattern as the example, especially if the animal has some EPD accuracy. Proven animals (accuracy .50 or better) will not see a significant EPD change. It is also important to remember these values are what we would expect to find with contemporary group data turned in on these animals. So the GeEPDs are mainly telling you the same information sooner than with current performance data.
How do I choose which animals to test using the Limousin Profiler?
All of your young, unproven animals are good candidates. Young herd bulls are perfect candidates since they account for 50 percent of the cow herd’s genetic potential and have very little accuracy. By having increased accuracy on replacement heifers, you get an advantage both sorting and mating cattle. Two- and three-year-old potential donor cows are good candidates since that don’t have a significant amount of accuracy. In breeds that have been using GeEPDs for a while, we are seeing an explosion of use. Whole bull sale offerings and entire replacement heifer groups are being run and breeders are demanding it run on potential herd bulls.
What about Lim-Flex?
Lim-Flex has proven to be a bit of a problem. The accuracy is not what we had first hoped it would be and what it needs to be to offer it commercially. We are currently running myostatin F94L tests on our entire discovery population in order to assess the potential interference we are getting and to hold it static in the genomic model. Look for further information and an announcement when that product becomes available.
Will the profiler accuracy improve?
We have seen in dairy breeds that the accuracy of genomic tests can become very high, but it takes a great number of samples and data. The prevalence of artificial insemination, number of records for each sire and number of genotypes on file has led to high accuracy. This can happen in Limousin, but it will take getting records on young cattle and continuing for generations.
Do I need to keep taking weights?
Definitely, the weights and data are the basis for how the Profiler is trained and it will have to be retrained almost continually to account for genetic shift and also new genotypes that are discovered. New weights also give updated magnitudes for genes and traits and will help us find more important genes and develop more focused, cheaper panels.
How do I take a sample and how much?
GeneSeek Inc., which offers the Limousin Profiler-Igenity enabled, prefers hair samples to blood. However, for the profiler, as well as any samples needing multiple tests, we need a large, quality hair sample. Use the rule of thumb—take a sample the width of your thumb from reasonably clean switch hair, pull in the opposite direction of hair growth, place follicle ends in hair card provided by NALF and send it to the NALF office. Getting a thumb-sized amount will also help decrease the number of resubmits you have for other tests. If you need hair cards, contact the NALF office.
If you have any further questions about the profiler or DNA services, please don’t hesitate to contact Brittany or myself in the NALF office.